join and burn

data/pars/fish_tags_joined.csv

@@ -0,0 +1,80 @@
+Species,Length,Weight,tag_row,date,tag_id
+Rainbow Trout,82,5.2,3,08-18-2021 13:03:42 01,3DD.003E1929FD. Row ID 3. 
+Rainbow Trout,38,0.6,,,
+Rainbow Trout,36,0.6,,,
+Rainbow Trout,118,11.5,4,08-18-2021 13:07:52 01,3DD.003E1929E6. Row ID 4. 
+Rainbow Trout,113,15.7,5,08-18-2021 13:10:39 01,3DD.003E1929F9. Row ID 5. 
+Rainbow Trout,129,23,6,08-18-2021 13:15:10 01,3DD.003E1929DF. Row ID 6. 
+Sculpin (General),78,4.4,,,
+Rainbow Trout,112,13.6,7,08-18-2021 13:17:22 01,3DD.003E1929D4. Row ID 7. 
+Rainbow Trout,135,25.3,8,08-18-2021 13:19:54 01,3DD.003E1929F7. Row ID 8. 
+Rainbow Trout,80,5.2,9,08-18-2021 13:56:36 01,3DD.003E1929F3. Row ID 9. 
+Rainbow Trout,40,0.7,,,
+Rainbow Trout,43,0.8,,,
+Rainbow Trout,109,14,10,08-18-2021 13:58:55 01,3DD.003E1929C1. Row ID 10. 
+Rainbow Trout,89,8.1,11,08-18-2021 14:01:05 01,3DD.003E1929F5. Row ID 11. 
+Rainbow Trout,91,8.2,12,08-18-2021 14:03:17 01,3DD.003E1929F4. Row ID 12. 
+Rainbow Trout,102,11.1,13,08-18-2021 15:08:39 01,3DD.003E1929EB. Row ID 13. 
+Rainbow Trout,39,0.7,,,
+Sculpin (General),48,1.6,,,
+Rainbow Trout,99,9.6,14,08-18-2021 15:10:33 01,3DD.003E1929E9. Row ID 14. 
+Rainbow Trout,121,18.6,15,08-18-2021 15:12:18 01,3DD.003E1929CE. Row ID 15. 
+Rainbow Trout,130,27.8,16,08-18-2021 15:14:48 01,3DD.003E1929FE. Row ID 16. 
+Rainbow Trout,89,7.8,17,08-18-2021 15:16:16 01,3DD.003E1929E3. Row ID 17. 
+Rainbow Trout,101,10.6,18,08-18-2021 15:19:17 01,3DD.003E1929D9. Row ID 18. 
+Rainbow Trout,89,7.5,19,08-18-2021 15:21:20 01,3DD.003E1929CD. Row ID 19. 
+Rainbow Trout,78,4.9,20,08-18-2021 15:23:44 01,3DD.003E1929C9. Row ID 20. 
+Rainbow Trout,82,6.2,21,08-18-2021 15:25:28 01,3DD.003E1929C5. Row ID 21. 
+Rainbow Trout,72,4.1,22,08-18-2021 15:28:16 01,3DD.003E1929D7. Row ID 22. 
+Sculpin (General),45,1.1,,,
+Rainbow Trout,96,9.4,23,08-18-2021 15:34:04 01,3DD.003E1929E0. Row ID 23. 
+Rainbow Trout,115,15.9,,,
+Rainbow Trout,108,13.3,24,08-18-2021 15:36:25 01,3DD.003E1929DE. Row ID 24. 
+Rainbow Trout,84,6.3,25,08-18-2021 15:38:58 01,3DD.003E1929D6. Row ID 25. 
+Sculpin (General),68,3.5,,,
+Rainbow Trout,89,8,26,08-18-2021 15:41:12 01,3DD.003E1929E5. Row ID 26. 
+Rainbow Trout,78,5.1,27,08-18-2021 15:43:00 01,3DD.003E1929FA. Row ID 27. 
+Rainbow Trout,105,12,28,08-18-2021 16:27:54 01,3DD.003E1929AF. Row ID 28. 
+Rainbow Trout,39,0.7,,,
+Rainbow Trout,43,0.9,,,
+Rainbow Trout,42,0.8,,,
+Rainbow Trout,43,0.8,,,
+Rainbow Trout,42,0.7,,,
+Rainbow Trout,44,1,,,
+Rainbow Trout,45,0.9,,,
+Rainbow Trout,34,0.5,,,
+Rainbow Trout,44,0.9,,,
+Rainbow Trout,44,0.9,,,
+Rainbow Trout,39,0.6,,,
+Rainbow Trout,40,0.7,,,
+Rainbow Trout,39,0.6,,,
+Rainbow Trout,49,1.3,,,
+Sculpin (General),61,2.5,,,
+Sculpin (General),56,1.7,,,
+Rainbow Trout,33,0.6,,,
+Rainbow Trout,45,0.8,,,
+Rainbow Trout,35,0.6,,,
+Rainbow Trout,41,0.7,,,
+Rainbow Trout,40,0.6,,,
+Rainbow Trout,45,0.9,,,
+Rainbow Trout,41,1,,,
+Rainbow Trout,39,1,,,
+Rainbow Trout,95,9.5,29,08-18-2021 16:29:14 01,3DD.003E1929C2. Row ID 29. 
+Rainbow Trout,98,9.4,30,08-18-2021 16:30:50 01,3DD.003E1929BC. Row ID 30. 
+Rainbow Trout,89,8,31,08-18-2021 16:32:13 01,3DD.003E1929DD. Row ID 31. 
+Rainbow Trout,98,10.6,32,08-18-2021 16:33:56 01,3DD.003E1929F8. Row ID 32. 
+Rainbow Trout,81,5.8,33,08-18-2021 16:57:23 01,3DD.003E1929AC. Row ID 33. 
+Sculpin (General),60,2.5,,,
+Sculpin (General),46,1.1,,,
+Rainbow Trout,37,1.4,,,
+Rainbow Trout,129,24.8,34,08-18-2021 16:58:55 01,3DD.003E1929BE. Row ID 34. 
+Rainbow Trout,109,14.5,35,08-18-2021 17:00:24 01,3DD.003E1929C6. Row ID 35. 
+Rainbow Trout,110,15.8,36,08-18-2021 17:01:53 01,3DD.003E1929B9. Row ID 36. 
+Rainbow Trout,95,9.8,37,08-18-2021 17:03:13 01,3DD.003E1929DA. Row ID 37. 
+Rainbow Trout,84,6,38,08-18-2021 17:04:47 01,3DD.003E1929CC. Row ID 38. 
+Rainbow Trout,89,8.3,39,,
+Rainbow Trout,98,9.5,,,
+Rainbow Trout,88,,,,
+Rainbow Trout,39,0.6,,,
+Rainbow Trout,79,,,,
+Rainbow Trout,109,,,,

scripts/pit_tags.R

@@ -1,26 +1,52 @@
 #combining pit tag data to individual fish data so that we can copy and paste directly into submission template
+# would be good to include the comments and times/camera of photos in the fish csv and then paste them to the right of the pit tag.
 
 source('scripts/packages.R')
 
 #import the pit tag csv
-path <- '../../repo/dff-2022/data/pars/tag_01_01.csv'
+# because we are working in a project our working directory is the root folder so all paths are
+# relative to that
+# path <- '../../repo/dff-2022/data/pars/tag_01_01.csv'
+path <- 'data/pars/tag_01_01.csv'
 
-pit_tag <- read.csv(path)
+# using readr is better than read.csv
+pit_tag <- readr::read_csv(path) %>%
+  #separate the pit tag out from the rest of the info in the pit tag csv
+  # https://stackoverflow.com/questions/66696779/separate-by-pattern-word-in-tidyr-and-dplyr
+  tidyr::separate(col=tag, into=c('date', 'tag_id'), sep='\\s*TAG\\s*') %>%
+  tibble::rowid_to_column()
 
-#separate the pit tag out from the rest of the info in the pit tag csv
-tags <- tidyr::separate(pit_tag, col=tag, into=c('date', 'tag_id'), sep=27)
-
-#generate row numbers
-rows <- dplyr::mutate(tags, id= row_number())
 
 #import csv with fish data
-path2 <- '../../repo/dff-2022/data/pars/fish_data.csv'
+path2 <- 'data/pars/fish_data.csv'
 
-fish <- read.csv(path2)
+fish <- readr::read_csv(path2)
 
 #join fish csv with pit tag csv based on tag row number
-dplyr::left_join(tags, fish, by=c("tag_row"="rows"))
-
-
+fish_tags <- dplyr::left_join(fish,
+                              pit_tag,
+                              by = c("tag_row" = "rowid")) %>%
+  # arrange columns
+  relocate(tag_id, .after = last_col()) %>%
+  # remove the first row because it was from the office. We need to pass the object piped to nrow as a "."
+  # as the first object gets passed to the slice function only
+  dplyr::slice(2:nrow(.)) %>%
+  # add a period, a space and the row number to the pit tag to go in the comments to make it easy to pull anything out we want later
+  dplyr::mutate(tag_id = case_when(
+    !is.na(tag_id) ~ paste0(tag_id, '. Row ID ', tag_row, '. '),
+    T ~ tag_id))
+
+# select a subsample of fish (lets go 15% since the sample size is small) to review manually to be sure the
+# pit tags match which fish they go with
+# set seed for reproducible sample - try running it again without setting the seed immediately before and see how it differs
+set.seed(1234)
+sample(nrow(fish_tags), nrow(fish_tags) * 0.15) %>%
+  # arrange the row numbers to make it easier to QA
+  sort()
+
+# burn the csv ready to cut and paste
+fish_tags %>%
+  readr::write_csv('data/pars/fish_tags_joined.csv',
+                   na = "" )